msp2db
Python package to create an SQLite database from a collection of MSP mass spectromertry spectra files. Currently works with MSP files formated as MassBank records or as MoNA records.
The resulting SQLite database can be used for spectral matching with msPurity Bioconductor R package, see vigenette.
Installation
$ pip install .
Command line
$ msp2db --msp_pth [msp file or directory of msp files] --source [name of source of msp e.g. massbank] --out_pth [out dir]
$ msp2db --help
usage: PROG [-h] -m MSP_PTH -s SOURCE [-o OUT_PTH] [-t TYPE] [-d] [-l MSLEVEL]
[-c CHUNK] [-x SCHEMA]
Convert msp to SQLite or MySQL database
optional arguments:
-h, --help show this help message and exit
-m MSP_PTH, --msp_pth MSP_PTH
path to the MSP file (or directory of msp files)
-s SOURCE, --source SOURCE
Name of data source (e.g. MassBank, LipidBlast)
-o OUT_PTH, --out_pth OUT_PTH
file path for SQLite database
-t TYPE, --db_type TYPE
database type [mysql, sqlite]
-d, --delete_tables delete tables
-l MSLEVEL, --mslevel MSLEVEL
ms level of fragmentation if not detailed in msp file
-c CHUNK, --chunk CHUNK
Chunks of spectra to parse data (useful to control
memory usage)
-x SCHEMA, --schema SCHEMA
Type of schema used (by default is "mona" msp style
but can use "massbank" style)
--------------
API
db_pth = 'spectral_library_07112018v1.db'
create_db(file_pth=db_pth, db_type='sqlite', db_name='spectra')
libdata = LibraryData(msp_pth='MoNA-export-FAHFA.msp',
db_pth=db_pth,
db_type='sqlite',
d_form=None,
schema='mona',
source='fahfa',
mslevel=None,
chunk=200)Developers & Contributors
Tom Lawson: t.n.lawson@bham.ac.uk
License
Released under the GNU General Public License v3.0 (see LICENSE file)